[Bioc-devel] Problem pushing new versions of xcms via git svn dcommit
Laurent Gatto
lg390 at cam.ac.uk
Tue Jan 3 22:10:40 CET 2017
Hi Steffen,
The usual
Commit to git as normal, when you want to push your commits to svn
1. `git checkout devel` to switch to the devel branch. (use release-X.X for
release branches)
2. `git svn rebase` to get the latest SVN changes.
3. `git merge master --log` to merge your changes from the master branch
or skip this step and work directly on the current branch.
4. `git svn dcommit --add-author-from` to sync and commit
your changes to svn.
worked out for me. Your latest commit #4b68af1d156b73 and #a03fba48f82b7
(updated NEWS file) have now been comitted to hedgehog.
I am not sure what is going on for you, but when I desperate with
git/git-svn, right before the nervous breakdown, I go for the 'have you
tried to turn it on and off again' solution, which generally works:
1) make sure you have comitted/pushed to Github and have a backup of any
files/dir you gitignore
2) rm -rf mzR
3) git clone git at github.com:sneumann/mzR.git
4) use update_remotes.sh
Let me know if there's anything I can help with.
Best wishes,
Laurent
On 2 January 2017 22:12, Steffen Neumann wrote:
> Hi all,and a happy new year!
>
> I am experiencing a lot of frustration getting changes from github
> pushed to BioC svn, and that includes some fixes for build issues
> in packages depending on xcms. I have tried several options:
>
> 1) git svn checkout, git remote add, git merge and git svn dcommit.
> 2) git clone github repo, update_remotes.shand git svn rebase
>
> both of which seem to fail due to the same reason,
> which seems to be somewhere around
>
> https://github.com/sneumann/xcms/commit/f9be4f4f23c49f56074670658bc9665e093c8f83
> Author: Steffen Neumann <sneumann at ipb-halle.de>
> Date:Fri Apr 1 14:09:29 2016 +0200
> Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave)
>
> I fail to fix these issues, and I am pretty frustrated
> since I fell into the git-svn tarpit not for the first time,
> it seems to be not fool-proof :-(
>
> Below are the details, hoping for help.
>
> Yours,
> Steffen
>
> 1) git svn checkout, git remote add, git merge and git svn dcommit.
>
> So, I have a fresh
>
> sneumann at acryl /vol/R/BioC/devel/xcms3 $ git svn checkout https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms
>
> Then I add the github remote:
>
> sneumann at acryl /vol/R/BioC/devel/xcms3/xcms (master) $ git remote add origin git at github.com:sneumann/xcms.git
> sneumann at acryl /vol/R/BioC/devel/xcms3/xcms (master) $ git fetch --tags
> remote: Counting objects: 1475, done.
> [...]
>>From github.com:sneumann/xcms
> * [new branch]devel-> origin/devel
> * [new branch]master-> origin/master
> * [new branch]xcms3-> origin/xcms3
>
> The devel branch is what I use to be in sync with BioC-SVN:
>
> sneumann at acryl /vol/R/BioC/devel/xcms3/xcms (master) $ git checkout devel
> Branch devel set up to track remote branch devel from origin.
> Switched to a new branch 'devel'
>
> sneumann at acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ git merge origin/xcms3
> Updating a4421c3..a112206
> Fast-forward
> DESCRIPTION|6 +-
> NAMESPACE|48 ++-
> R/AllGenerics.R|38 +-
> [...]
> vignettes/new_functionality.org|88 ++++-
> 41 files changed, 4890 insertions(+), 2250 deletions(-)
>
> sneumann at acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ git svn dcommit
> Committing to https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms ...
> D R/00Generics.R
>
> ERROR from SVN:
> Filesystem has no item: '/bioconductor/!svn/txr/125556-1/trunk/madman/Rpacks/xcms/R/00Generics.R' path not found
> W: a1122065a96cf6e69088417d82fe987cda188cd5 and refs/remotes/git-svn differ, using rebase:
> :100644 100644 d36b142908ab4507e95d495d3ec450008a210e8f a3f97d8f779d878b86a73d534415e679415e90f3 M DESCRIPTION
> :100755 100755 a58677bbe186fea1447948c7286bc47d04735efc fe69bdd2e969a906fac87d4bddd64bd90258f0cd M NAMESPACE
> :040000 040000 2f5317b4c96f1d267b43ef8deba1532df6cb56db c760aa2196632e99c0e0e59ed9700b27cb001fa3 M R
> :040000 040000 45a9a220d96c3cdabe03cd8792dfc9628f058dab e89e65a3eb7db9d6590c12b8fb94306811557789 M inst
> :040000 040000 8284909b39e4d90eb957aadc26f92a8df9907cb2 125b7635684f73f65185aea52a7564c11bf187c5 M man
> :040000 040000 da9a1c166e3df0c13cd3ea61e44356039b649cd2 dbee4fedf371d6570b91cc7f50fe930294eac1f2 M vignettes
> First, rewinding head to replay your work on top of it...
> Applying: Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave)
> Using index info to reconstruct a base tree...
> A R/xcmsRaw.R
> .git/rebase-apply/patch:37: trailing whitespace.
> scan <- getScan(object, scan=i)
> .git/rebase-apply/patch:82: trailing whitespace.
> xr at env$mz[1:length(o)] <- scan[o, "mz"]
> .git/rebase-apply/patch:83: trailing whitespace.
> xr at env$intensity[1:length(o)] <- scan[o, "intensity"]
> .git/rebase-apply/patch:88: trailing whitespace.
>
> .git/rebase-apply/patch:90: new blank line at EOF.
> +
> warning: 5 lines add whitespace errors.
> Falling back to patching base and 3-way merge...
> Auto-merging inst/unitTests/runit.findPeaksCentWave.R
> CONFLICT (add/add): Merge conflict in inst/unitTests/runit.findPeaksCentWave.R
> CONFLICT (modify/delete): R/xcmsRaw.R deleted in 4c6815a9b4f985658f19824dde21748e49b5dad0 and modified in Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave). Version Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave) of R/xcmsRaw.R left in tree.
> error: Failed to merge in the changes.
> Patch failed at 0001 Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave)
> The copy of the patch that failed is found in: .git/rebase-apply/patch
>
> When you have resolved this problem, run "git rebase --continue".
> If you prefer to skip this patch, run "git rebase --skip" instead.
> To check out the original branch and stop rebasing, run "git rebase --abort".
>
> rebase refs/remotes/git-svn: command returned error: 128
>
>
>
> -----------------------------------------------------------------------------
>
> 2) git clone github repo, update_remotes.shand git svn rebase
>
>
> sneumann at acryl /vol/R/BioC/devel/xcms3 $ git clone git at github.com:sneumann/xcms.git
> Cloning into 'xcms'...
> remote: Counting objects: 6343, done.
> remote: Compressing objects: 100% (188/188), done.
> remote: Total 6343 (delta 124), reused 0 (delta 0), pack-reused 6155
> Receiving objects: 100% (6343/6343), 3.74 MiB | 1.39 MiB/s, done.
> Resolving deltas: 100% (4806/4806), done.
> Checking connectivity... done.
>
> sneumann at acryl /vol/R/BioC/devel/xcms3 $ cd xcms
> sneumann at acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ ../update_remotes.sh
> Enter passphrase for key '/home/sneumann/.ssh/id_rsa':
> devel already exists, create a custom branch to track bioc/master with
> `git branch --track NEW_NAME bioc/master`
> Commit to git as normal, when you want to push your commits to svn
> 1. `git checkout devel` to switch to the devel branch. (use release-X.X for
> release branches)
> 2. `git svn rebase` to get the latest SVN changes.
> 3. `git merge master --log` to merge your changes from the master branch
> or skip this step and work directly on the current branch.
> 4. `git svn dcommit --add-author-from` to sync and commit
> your changes to svn.
>
> sneumann at acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ git branch --track biocmaster bioc/master
> Branch biocmaster set up to track remote branch master from bioc.
>
> sneumann at acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ git svn rebase
> Migrating from a git-svn v1 layout...
> Data from a previous version of git-svn exists, but
> .git/svn
> (required for this version (2.7.4) of git-svn) does not exist.
> Done migrating from a git-svn v1 layout
> Rebuilding .git/svn/refs/remotes/git-svn-devel/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358 ...
> r11695 = 612044c47521e079cf31425550729010d9654abc
> [...]
> r125419 = 4c6815a9b4f985658f19824dde21748e49b5dad0
> Done rebuilding .git/svn/refs/remotes/git-svn-devel/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358
>
> First, rewinding head to replay your work on top of it...
> Applying: Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave)
> Using index info to reconstruct a base tree...
> A R/xcmsRaw.R
> .git/rebase-apply/patch:37: trailing whitespace.
> scan <- getScan(object, scan=i)
> .git/rebase-apply/patch:82: trailing whitespace.
> xr at env$mz[1:length(o)] <- scan[o, "mz"]
> .git/rebase-apply/patch:83: trailing whitespace.
> xr at env$intensity[1:length(o)] <- scan[o, "intensity"]
> .git/rebase-apply/patch:88: trailing whitespace.
>
> .git/rebase-apply/patch:90: new blank line at EOF.
> +
> warning: 5 lines add whitespace errors.
> Falling back to patching base and 3-way merge...
> Auto-merging inst/unitTests/runit.findPeaksCentWave.R
> CONFLICT (add/add): Merge conflict in inst/unitTests/runit.findPeaksCentWave.R
> CONFLICT (modify/delete): R/xcmsRaw.R deleted in 4c6815a9b4f985658f19824dde21748e49b5dad0 and modified in Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave). Version Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave) of R/xcmsRaw.R left in tree.
> error: Failed to merge in the changes.
> Patch failed at 0001 Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave)
> The copy of the patch that failed is found in: .git/rebase-apply/patch
>
> When you have resolved this problem, run "git rebase --continue".
> If you prefer to skip this patch, run "git rebase --skip" instead.
> To check out the original branch and stop rebasing, run "git rebase --abort".
>
> rebase refs/remotes/git-svn-devel: command returned error: 128
--
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/
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